Contacts of the helix formed by residues 2 - 20 (chain B) in PDB entry 4RHW
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 2 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 1.3 79.8 - - - +
3B ALA* 1.3 65.7 + - - +
4B LYS* 3.3 7.4 - - + +
5B ALA* 3.3 9.6 + - + +
6B ARG* 3.1 17.7 + - - +
65B ASN* 2.9 33.4 + - - +
92B PRO* 3.4 23.5 - - + +
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Residues in contact with ALA 3 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET 3.7 0.8 + - - -
2B ASP* 1.3 71.0 - - - +
4B LYS* 1.3 67.4 + - - +
6B ARG* 3.3 7.5 + - - +
7B ASN* 2.9 26.1 + - - +
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Residues in contact with LYS 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B ASP* 3.3 5.3 - - + +
3B ALA* 1.3 80.3 - - - +
5B ALA* 1.3 61.5 + - - +
7B ASN* 3.6 7.9 + - - +
8B CYS* 3.0 24.2 + - + +
89B ASP* 3.6 31.2 + - - +
90B GLY* 4.6 8.2 - - - +
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Residues in contact with ALA 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 3.7 24.0 - - + -
2B ASP* 3.3 16.6 + - + +
3B ALA 3.2 0.6 - - - -
4B LYS* 1.3 78.8 - - - +
6B ARG* 1.3 63.2 + - - +
8B CYS* 3.1 13.4 + - - +
9B LEU* 3.1 10.4 + - - +
68B TYR* 3.3 15.9 - - + -
90B GLY 3.6 21.4 + - - +
92B PRO* 4.3 12.3 - - + -
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Residues in contact with ARG 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 3.5 22.9 - - + +
2B ASP 3.1 8.7 + - - +
3B ALA* 3.6 9.6 - - - +
5B ALA* 1.3 77.9 - - - +
7B ASN* 1.3 65.1 + - - +
9B LEU* 3.1 8.7 + - - +
10B LEU* 3.0 56.9 + - - +
61B LEU* 3.9 39.9 + - + +
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Residues in contact with ASN 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B ALA 2.9 18.6 + - - +
4B LYS* 3.8 7.2 + - - +
6B ARG* 1.3 77.0 - - - +
8B CYS* 1.3 56.8 + - - +
10B LEU* 3.2 16.9 + - - +
11B GLN* 2.9 57.1 + - - +
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Residues in contact with CYS 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B LYS* 3.0 15.3 + - + +
5B ALA 3.2 10.1 - - - +
7B ASN* 1.3 78.6 - - - +
9B LEU* 1.3 61.4 + - - +
11B GLN* 3.4 13.6 + - - -
12B HIS* 3.0 32.5 - - - -
68B TYR* 3.4 20.6 - - - +
86B LEU 3.8 22.4 - - - -
87B LEU* 4.0 4.6 - - - +
89B ASP* 4.9 2.7 - - - -
90B GLY* 3.8 17.9 - - - -
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Residues in contact with LEU 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 4.9 2.7 - - - -
5B ALA 3.1 4.3 + - - +
6B ARG 3.1 10.7 + - - +
8B CYS* 1.3 77.3 - - - +
10B LEU* 1.3 66.2 + - - +
12B HIS* 3.2 3.1 + - - +
13B ARG* 2.9 25.4 + - - +
16B LEU* 4.6 4.4 - - + +
57B ILE* 3.8 24.7 - - + -
60B ILE* 4.3 18.8 - - + -
61B LEU* 3.7 25.6 - - + -
68B TYR* 3.4 33.0 - - + -
71B PHE* 4.3 16.4 - - + -
87B LEU* 4.0 24.0 - - + -
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Residues in contact with LEU 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ARG* 3.0 43.6 + - - +
7B ASN* 3.5 17.7 - - - +
9B LEU* 1.3 77.6 - - - +
11B GLN* 1.3 63.2 + - - +
12B HIS 3.2 0.9 + - - -
13B ARG* 3.4 49.5 + - - +
61B LEU* 3.8 23.6 - - + -
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Residues in contact with GLN 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ASN* 2.9 39.4 + - - +
8B CYS* 3.5 15.1 - - - +
9B LEU 3.3 0.2 - - - -
10B LEU* 1.3 76.6 - - - +
12B HIS* 1.3 83.6 + - + +
13B ARG 3.6 0.4 + - - -
14B GLU* 5.3 1.0 + - - +
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Residues in contact with HIS 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B CYS* 3.0 29.8 + - - +
9B LEU 3.2 4.3 + - - -
10B LEU 3.2 0.6 - - - -
11B GLN* 1.3 104.5 + - + +
13B ARG* 1.3 64.9 + - - +
14B GLU 3.1 4.1 + - - -
15B ALA* 3.2 7.0 + - + +
16B LEU* 3.1 35.4 + - + +
86B LEU* 3.4 61.4 + - + +
87B LEU* 3.9 8.5 - - + -
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Residues in contact with ARG 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B LEU 2.9 14.5 + - - +
10B LEU* 3.4 37.1 + - - +
11B GLN 3.6 0.4 - - - -
12B HIS* 1.3 77.1 - - - +
14B GLU* 1.3 63.3 + - + +
16B LEU* 3.4 8.5 + - - +
17B GLU* 3.0 38.1 + - - +
54B ALA 5.2 0.8 + - - -
57B ILE* 3.7 25.0 - - + +
58B LYS* 4.0 22.2 - - - +
61B LEU* 3.5 24.6 - - - +
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Residues in contact with GLU 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B GLN 5.3 1.1 + - - +
12B HIS 3.1 0.8 - - - -
13B ARG* 1.3 82.9 - - + +
15B ALA* 1.3 66.7 + - - +
17B GLU* 3.3 14.0 + - - +
18B LYS* 2.9 59.8 + - - +
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Residues in contact with ALA 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B HIS* 3.2 11.2 + - + +
14B GLU* 1.3 80.7 - - - +
16B LEU* 1.3 63.2 + - - +
18B LYS* 3.5 10.6 + - - +
19B ASP* 3.2 24.1 + - - +
83B LEU* 3.9 16.6 - - + +
86B LEU* 4.3 14.8 - - + -
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Residues in contact with LEU 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 4.6 8.3 - - + +
12B HIS* 3.1 28.6 + - + +
13B ARG* 3.6 8.3 - - - +
15B ALA* 1.3 76.1 - - - +
17B GLU* 1.3 62.1 + - - +
18B LYS 3.3 0.2 + - - -
19B ASP 3.3 1.0 + - - -
20B ILE* 3.2 35.0 + - + +
57B ILE* 4.0 13.5 - - + -
71B PHE* 4.4 15.7 - - + -
75B LEU* 3.8 32.5 - - + -
83B LEU* 4.1 27.1 - - + +
86B LEU* 6.5 0.4 - - + -
87B LEU* 4.1 26.5 - - + -
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Residues in contact with GLU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ARG* 3.0 24.9 + - - +
14B GLU* 3.3 15.8 + - - +
16B LEU* 1.3 74.9 - - - +
18B LYS* 1.3 53.5 + - - +
49B GLN* 2.8 32.9 + - - +
50B GLN* 3.8 34.7 + - + +
53B ALA* 3.6 11.9 - - - +
54B ALA* 2.9 46.8 - - - +
57B ILE* 4.0 6.2 - - + +
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Residues in contact with LYS 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B GLU* 2.9 49.9 + - + +
15B ALA* 3.8 4.9 - - - +
16B LEU 3.2 0.8 - - - -
17B GLU* 1.3 77.3 - - - +
19B ASP* 1.3 72.6 + - - +
49B GLN* 3.9 11.8 + - - +
50B GLN* 4.3 22.0 - - - +
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Residues in contact with ASP 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ALA* 3.2 16.5 - - - +
16B LEU 3.3 2.2 + - - -
18B LYS* 1.3 91.8 - - - +
20B ILE* 1.3 64.9 + - - +
21B LYS 3.7 1.2 + - - -
49B GLN* 4.4 0.7 - - - -
80B TYR* 3.8 14.9 + - + -
83B LEU* 3.8 30.0 - - + +
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Residues in contact with ILE 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LEU* 3.2 24.8 + - + +
18B LYS 3.9 0.4 - - - -
19B ASP* 1.3 75.2 - - - +
21B LYS* 1.3 60.1 + - - +
22B THR* 3.4 19.7 + - + +
25B ILE* 4.5 15.5 - - + -
49B GLN* 2.9 27.9 + - - +
53B ALA* 4.0 18.4 - - + +
56B LEU* 4.5 8.1 - - + -
57B ILE* 5.4 3.8 - - + -
71B PHE* 4.5 23.8 - - + -
75B LEU* 4.0 17.5 - - + -
80B TYR* 3.8 8.5 - - + -
83B LEU* 3.8 21.8 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il